1. singleCellTK
  2. R
  3. importMultipleSources.R
Browse code

Added more unit tests

Yichen Wang authored on 28/06/2022 20:51:30
Showing1 changed files
R/importMultipleSources.R
History View file @976db8699
... ... 
@@ -44,7 +44,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
44 44 
     } else if (entry$type == "starSolo") {
45 45 
       newSce <- importSTARsolo(
46 46 
         STARsoloDirs = entry$params$STARsoloDirs,
47 
-        samples = entry$params$amples,
47 
+        samples = entry$params$samples,
48 48 
         delayedArray = delayedArray
49 49 
       )
50 50 
     } else if (entry$type == "busTools") {
... ... 
@@ -96,7 +96,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
96 96 
       }
97 97
98 98 
     }
99 
-
99 
+
100 100 
     # Begin Set Tags
101 101 
     if(entry$type %in% c("cellRanger2", "cellRanger3", "starSolo", "busTools", "seqc", "optimus", "example")){
102 102 
       newSce <- expSetDataTag(
... ... 
@@ -114,7 +114,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
114 114 
             assayType = "raw",
115 115 
             assays = "counts")
116 116 
         }, silent = TRUE)
117 
-
117 
+
118 118 
         try({
119 119 
           logcounts(newSce)
120 120 
           newSce <- expSetDataTag(
... ... 
@@ -122,7 +122,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
122 122 
             assayType = "transformed",
123 123 
             assays = "logcounts")
124 124 
         }, silent = TRUE)
125 
-
125 
+
126 126 
         try({
127 127 
           normcounts(newSce)
128 128 
           newSce <- expSetDataTag(
... ... 
@@ -130,7 +130,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
130 130 
             assayType = "transformed",
131 131 
             assays = "normcounts")
132 132 
         }, silent = TRUE)
133 
-
133 
+
134 134 
         try({
135 135 
           celda::decontXcounts(newSce)
136 136 
           newSce <- expSetDataTag(
... ... 
@@ -138,21 +138,21 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
138 138 
             assayType = "raw",
139 139 
             assays = "decontXcounts")
140 140 
         }, silent = TRUE)
141 
-
141 
+
142 142 
         untaggedAssays <- SummarizedExperiment::assayNames(newSce)
143 143 
         untaggedAssays <- untaggedAssays[! untaggedAssays %in% c('counts', 'logcounts', 'normcounts', 'decontX')]
144 
-
144 
+
145 145 
         newSce <- expSetDataTag(
146 146 
           inSCE = newSce,
147 147 
           assayType = "uncategorized",
148 
-          assays = untaggedAssays)
148 
+          assays = untaggedAssays)
149 149 
       }
150 150 
       # End Set Tags
151 151 
     }
152 
-
152 
+
153 153 
     sceObjs = c(sceObjs, list(newSce))
154 154 
   }
155 
-
155 
+
156 156 
   return(combineSCE(sceList = sceObjs,
157 157 
                     by.r = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(rowData(x))})),
158 158 
                     by.c = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
Browse code

Fix UI bug: set Ref for cellRangerV2 importing

Yichen Wang authored on 09/11/2021 16:39:22
Showing1 changed files
R/importMultipleSources.R
History View file @a765c34bf
... ... 
@@ -21,7 +21,8 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
21 21 
           cellRangerDirs = entry$params$cellRangerDirs,
22 22 
           sampleDirs = entry$params$sampleDirs,
23 23 
           sampleNames = entry$params$sampleNames,
24 
-          delayedArray = delayedArray
24 
+          delayedArray = delayedArray,
25 
+          reference = entry$params$reference
25 26 
         )
26 27 
       }
27 28
Browse code

BiocCheck fixing errors/warnings!

Irzam Sarfraz authored on 14/10/2021 10:24:48
Showing1 changed files
R/importMultipleSources.R
History View file @3077c99ec
... ... 
@@ -105,7 +105,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
105 105 
     }
106 106 
     else if(entry$type %in% c("rds", "files")){
107 107 
       # Check if tags already stored in uploaded rds/files
108 
-      if(is.null(metadata(newSce)$assayType)){
108 
+      if(is.null(S4Vectors::metadata(newSce)$assayType)){
109 109 
         try({
110 110 
           counts(newSce)
111 111 
           newSce <- expSetDataTag(
Browse code

Introducing bioc error to test if bioccheck breaks!

Irzam Sarfraz authored on 14/10/2021 10:12:03
Showing1 changed files
R/importMultipleSources.R
History View file @cc4b4a796
... ... 
@@ -105,7 +105,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
105 105 
     }
106 106 
     else if(entry$type %in% c("rds", "files")){
107 107 
       # Check if tags already stored in uploaded rds/files
108 
-      if(is.null(S4Vectors::metadata(newSce)$assayType)){
108 
+      if(is.null(metadata(newSce)$assayType)){
109 109 
         try({
110 110 
           counts(newSce)
111 111 
           newSce <- expSetDataTag(
Browse code

Fixed BioC errors & warnings

Irzam Sarfraz authored on 13/10/2021 17:56:28
Showing1 changed files
R/importMultipleSources.R
History View file @208bb946b
... ... 
@@ -101,11 +101,11 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
101 101 
       newSce <- expSetDataTag(
102 102 
         inSCE = newSce,
103 103 
         assayType = "raw",
104 
-        assays = assayNames(newSce))
104 
+        assays = SummarizedExperiment::assayNames(newSce))
105 105 
     }
106 106 
     else if(entry$type %in% c("rds", "files")){
107 107 
       # Check if tags already stored in uploaded rds/files
108 
-      if(is.null(metadata(newSce)$assayType)){
108 
+      if(is.null(S4Vectors::metadata(newSce)$assayType)){
109 109 
         try({
110 110 
           counts(newSce)
111 111 
           newSce <- expSetDataTag(
... ... 
@@ -131,14 +131,14 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
131 131 
         }, silent = TRUE)
132 132
133 133 
         try({
134 
-          decontXcounts(newSce)
134 
+          celda::decontXcounts(newSce)
135 135 
           newSce <- expSetDataTag(
136 136 
             inSCE = newSce,
137 137 
             assayType = "raw",
138 138 
             assays = "decontXcounts")
139 139 
         }, silent = TRUE)
140 140
141 
-        untaggedAssays <- assayNames(newSce)
141 
+        untaggedAssays <- SummarizedExperiment::assayNames(newSce)
142 142 
         untaggedAssays <- untaggedAssays[! untaggedAssays %in% c('counts', 'logcounts', 'normcounts', 'decontX')]
143 143
144 144 
         newSce <- expSetDataTag(
Browse code

Updated tags

Irzam Sarfraz authored on 09/10/2021 21:13:47
Showing1 changed files
R/importMultipleSources.R
History View file @5b1a0160b
... ... 
@@ -95,8 +95,63 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
95 95 
       }
96 96
97 97 
     }
98 
+
99 
+    # Begin Set Tags
100 
+    if(entry$type %in% c("cellRanger2", "cellRanger3", "starSolo", "busTools", "seqc", "optimus", "example")){
101 
+      newSce <- expSetDataTag(
102 
+        inSCE = newSce,
103 
+        assayType = "raw",
104 
+        assays = assayNames(newSce))
105 
+    }
106 
+    else if(entry$type %in% c("rds", "files")){
107 
+      # Check if tags already stored in uploaded rds/files
108 
+      if(is.null(metadata(newSce)$assayType)){
109 
+        try({
110 
+          counts(newSce)
111 
+          newSce <- expSetDataTag(
112 
+            inSCE = newSce,
113 
+            assayType = "raw",
114 
+            assays = "counts")
115 
+        }, silent = TRUE)
116 
+
117 
+        try({
118 
+          logcounts(newSce)
119 
+          newSce <- expSetDataTag(
120 
+            inSCE = newSce,
121 
+            assayType = "transformed",
122 
+            assays = "logcounts")
123 
+        }, silent = TRUE)
124 
+
125 
+        try({
126 
+          normcounts(newSce)
127 
+          newSce <- expSetDataTag(
128 
+            inSCE = newSce,
129 
+            assayType = "transformed",
130 
+            assays = "normcounts")
131 
+        }, silent = TRUE)
132 
+
133 
+        try({
134 
+          decontXcounts(newSce)
135 
+          newSce <- expSetDataTag(
136 
+            inSCE = newSce,
137 
+            assayType = "raw",
138 
+            assays = "decontXcounts")
139 
+        }, silent = TRUE)
140 
+
141 
+        untaggedAssays <- assayNames(newSce)
142 
+        untaggedAssays <- untaggedAssays[! untaggedAssays %in% c('counts', 'logcounts', 'normcounts', 'decontX')]
143 
+
144 
+        newSce <- expSetDataTag(
145 
+          inSCE = newSce,
146 
+          assayType = "uncategorized",
147 
+          assays = untaggedAssays)
148 
+      }
149 
+      # End Set Tags
150 
+    }
151 
+
98 152 
     sceObjs = c(sceObjs, list(newSce))
99 153 
   }
154 
+
100 155 
   return(combineSCE(sceList = sceObjs,
101 156 
                     by.r = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(rowData(x))})),
102 157 
                     by.c = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
Browse code

UI update for previous related DE function update; plus many minor bug fixes

Yichen Wang authored on 17/03/2021 16:51:52
Showing1 changed files
R/importMultipleSources.R
History View file @ea2808fc7
... ... 
@@ -24,7 +24,7 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
24 24 
           delayedArray = delayedArray
25 25 
         )
26 26 
       }
27 
-
27 
+
28 28 
     } else if (entry$type == "cellRanger3") {
29 29 
       if (is.null(entry$params$cellRangerDirs)) {
30 30 
         newSce <- importCellRangerV3Sample(
... ... 
@@ -93,11 +93,10 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
93 93 
           SummarizedExperiment::assay(newSce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(newSce, assay))
94 94 
         }
95 95 
       }
96 
-
96 
+
97 97 
     }
98 98 
     sceObjs = c(sceObjs, list(newSce))
99 99 
   }
100 
-
101 100 
   return(combineSCE(sceList = sceObjs,
102 101 
                     by.r = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(rowData(x))})),
103 102 
                     by.c = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
Browse code

Update importMitoGeneSet function. Change delayedArray=False for all import function. Minor fixs in QC HTML report

rz2333 authored on 30/12/2020 17:40:20
Showing1 changed files
R/importMultipleSources.R
History View file @969718f95
... ... 
@@ -2,7 +2,7 @@
2 2 
 #' Imports samples from different sources and compiles them into a list of SCE objects
3 3 
 #' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)
4 4 
 #' @param delayedArray Boolean. Whether to read the expression matrix as
5 
-#'  \link{DelayedArray} object or not. Default \code{TRUE}.
5 
+#'  \link{DelayedArray} object or not. Default \code{FALSE}.
6 6 
 #' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
7 7 
 #' the droplet or cell data or both,depending on the dataType that users provided.
8 8 
 #' @export
Browse code

Edit links to documentation

unknown authored on 22/10/2020 03:39:09
Showing1 changed files
R/importMultipleSources.R
History View file @6fe21ae1e
... ... 
@@ -2,7 +2,7 @@
2 2 
 #' Imports samples from different sources and compiles them into a list of SCE objects
3 3 
 #' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)
4 4 
 #' @param delayedArray Boolean. Whether to read the expression matrix as
5 
-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
5 
+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
6 6 
 #' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
7 7 
 #' the droplet or cell data or both,depending on the dataType that users provided.
8 8 
 #' @export
Browse code

Fix bugs in importMultipleSources.R. Update QC documentation

rz2333 authored on 19/10/2020 02:08:45
Showing1 changed files
R/importMultipleSources.R
History View file @cc7d9f647
... ... 
@@ -85,12 +85,12 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
85 85 
       }
86 86
87 87 
       for(assay in SummarizedExperiment::assayNames(newSce)) {
88 
-        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
89 
-          SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
88 
+        if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
89 
+          SummarizedExperiment::assay(newSce, assay) <- .convertToMatrix(SummarizedExperiment::assay(newSce, assay))
90 90 
         }
91 91
92 
-        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "DelayedArray") && isTRUE(delayedArray)) {
93 
-          SummarizedExperiment::assay(sce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(sce, assay))
92 
+        if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "DelayedArray") && isTRUE(delayedArray)) {
93 
+          SummarizedExperiment::assay(newSce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(newSce, assay))
94 94 
         }
95 95 
       }
96 96
Browse code

merge master into sctk_qc

rz2333 authored on 15/10/2020 20:55:34
Showing0 changed files
Browse code

Update SCTK_QC, importAnnData and sce2adata.R

rz2333 authored on 15/10/2020 16:02:58
Showing1 changed files
R/importMultipleSources.R
History View file @ac1737659
... ... 
@@ -4,7 +4,7 @@
4 4 
 #' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
5 5 
 #' the droplet or cell data or both,depending on the dataType that users provided.
6 6 
 #' @export
7 
-importMultipleSources <- function(allImportEntries) {
7 
+importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
8 8 
   sceObjs <- list()
9 9 
   for (entry in allImportEntries$samples) {
10 10 
     if (entry$type == "cellRanger2") {
... ... 
@@ -12,12 +12,14 @@ importMultipleSources <- function(allImportEntries) {
12 12 
         newSce <- importCellRangerV2Sample(
13 13 
           dataDir = entry$params$dataDir,
14 14 
           sampleName = entry$params$sampleName,
15 
+          delayedArray = delayedArray
15 16 
         )
16 17 
       } else {
17 18 
         newSce <- importCellRangerV2(
18 19 
           cellRangerDirs = entry$params$cellRangerDirs,
19 20 
           sampleDirs = entry$params$sampleDirs,
20 21 
           sampleNames = entry$params$sampleNames,
22 
+          delayedArray = delayedArray
21 23 
         )
22 24 
       }
23 25
... ... 
@@ -26,42 +28,50 @@ importMultipleSources <- function(allImportEntries) {
26 28 
         newSce <- importCellRangerV3Sample(
27 29 
           dataDir = entry$params$dataDir,
28 30 
           sampleName = entry$params$sampleName,
31 
+          delayedArray = delayedArray
29 32 
         )
30 33 
       } else {
31 34 
         newSce <- importCellRangerV3(
32 35 
           cellRangerDirs = entry$params$cellRangerDirs,
33 36 
           sampleDirs = entry$params$sampleDirs,
34 37 
           sampleNames = entry$params$sampleNames,
38 
+          delayedArray = delayedArray
35 39 
         )
36 40 
       }
37 41 
     } else if (entry$type == "starSolo") {
38 42 
       newSce <- importSTARsolo(
39 43 
         STARsoloDirs = entry$params$STARsoloDirs,
40 
-        samples = entry$params$amples
44 
+        samples = entry$params$amples,
45 
+        delayedArray = delayedArray
41 46 
       )
42 47 
     } else if (entry$type == "busTools") {
43 48 
       newSce <- importBUStools(
44 49 
         BUStoolsDirs = entry$params$BUStoolsDirs,
45 50 
         samples = entry$params$samples,
51 
+        delayedArray = delayedArray
46 52 
       )
47 53 
     } else if (entry$type == "seqc") {
48 54 
       newSce <- importSEQC(
49 55 
         seqcDirs = entry$params$seqcDirs,
50 56 
         samples = entry$params$samples,
51 57 
         prefix = entry$params$prefix,
58 
+        delayedArray = delayedArray
52 59 
       )
53 60 
     } else if (entry$type == "optimus") {
54 61 
       newSce <- importOptimus(
55 62 
         OptimusDirs = entry$params$OptimusDirs,
56 
-        samples = entry$params$samples
63 
+        samples = entry$params$samples,
64 
+        delayedArray = delayedArray
57 65 
       )
58 66 
     } else if (entry$type == "files") {
59 67 
       newSce <- importFromFiles(assayFile = entry$params$assayFile,
60 68 
                                 annotFile = entry$params$annotFile,
61 69 
                                 featureFile = entry$params$featureFile,
62 
-                                assayName = entry$params$assayName)
70 
+                                assayName = entry$params$assayName,
71 
+                                delayedArray = delayedArray)
63 72 
     } else if (entry$type == "example") {
64 
-      newSce <- importExampleData(dataset = entry$params$dataset)
73 
+      newSce <- importExampleData(dataset = entry$params$dataset,
74 
+                                  delayedArray = delayedArray)
65 75 
     } else if (entry$type == "rds") {
66 76 
       importedrds <- readRDS(entry$params$rdsFile)
67 77 
       if (base::inherits(importedrds, "SummarizedExperiment")) {
... ... 
@@ -71,13 +81,24 @@ importMultipleSources <- function(allImportEntries) {
71 81 
       } else {
72 82 
         stop("The '.rds' file should contain a 'SingleCellExperiment' or 'Seurat' object.")
73 83 
       }
84 
+
85 
+      for(assay in SummarizedExperiment::assayNames(newSce)) {
86 
+        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
87 
+          SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
88 
+        }
89 
+
90 
+        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "DelayedArray") && isTRUE(delayedArray)) {
91 
+          SummarizedExperiment::assay(sce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(sce, assay))
92 
+        }
93 
+      }
94 
+
74 95 
     }
75 96 
     sceObjs = c(sceObjs, list(newSce))
76 97 
   }
77 98
78 99 
   return(combineSCE(sceList = sceObjs,
79 
-                    by.r = NULL,
80 
-                    by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
100 
+                    by.r = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(rowData(x))})),
101 
+                    by.c = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
81 102 
                     combined = TRUE)
82 103 
   )
83 104 
 }
Browse code

Changed all T/F to TRUE/FALSE

Joshua D. Campbell authored on 13/10/2020 02:45:44
Showing1 changed files
R/importMultipleSources.R
History View file @9cafccf81
... ... 
@@ -78,7 +78,7 @@ importMultipleSources <- function(allImportEntries) {
78 78 
   return(combineSCE(sceList = sceObjs,
79 79 
                     by.r = NULL,
80 80 
                     by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
81 
-                    combined = T)
81 
+                    combined = TRUE)
82 82 
   )
83 83 
 }
84 84
Browse code

Updated description in DESCRIPTION. Moved importMultipleSources to its own file and removed some shiny code. Updated docs.

Joshua D. Campbell authored on 12/10/2020 18:25:27
Showing1 changed files
R/importMultipleSources.R
History View file @31390a703
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,84 @@
1 
+
2 
+#' Imports samples from different sources and compiles them into a list of SCE objects
3 
+#' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)
4 
+#' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
5 
+#' the droplet or cell data or both,depending on the dataType that users provided.
6 
+#' @export
7 
+importMultipleSources <- function(allImportEntries) {
8 
+  sceObjs <- list()
9 
+  for (entry in allImportEntries$samples) {
10 
+    if (entry$type == "cellRanger2") {
11 
+      if (is.null(entry$params$cellRangerDirs)) {
12 
+        newSce <- importCellRangerV2Sample(
13 
+          dataDir = entry$params$dataDir,
14 
+          sampleName = entry$params$sampleName,
15 
+        )
16 
+      } else {
17 
+        newSce <- importCellRangerV2(
18 
+          cellRangerDirs = entry$params$cellRangerDirs,
19 
+          sampleDirs = entry$params$sampleDirs,
20 
+          sampleNames = entry$params$sampleNames,
21 
+        )
22 
+      }
23 
+
24 
+    } else if (entry$type == "cellRanger3") {
25 
+      if (is.null(entry$params$cellRangerDirs)) {
26 
+        newSce <- importCellRangerV3Sample(
27 
+          dataDir = entry$params$dataDir,
28 
+          sampleName = entry$params$sampleName,
29 
+        )
30 
+      } else {
31 
+        newSce <- importCellRangerV3(
32 
+          cellRangerDirs = entry$params$cellRangerDirs,
33 
+          sampleDirs = entry$params$sampleDirs,
34 
+          sampleNames = entry$params$sampleNames,
35 
+        )
36 
+      }
37 
+    } else if (entry$type == "starSolo") {
38 
+      newSce <- importSTARsolo(
39 
+        STARsoloDirs = entry$params$STARsoloDirs,
40 
+        samples = entry$params$amples
41 
+      )
42 
+    } else if (entry$type == "busTools") {
43 
+      newSce <- importBUStools(
44 
+        BUStoolsDirs = entry$params$BUStoolsDirs,
45 
+        samples = entry$params$samples,
46 
+      )
47 
+    } else if (entry$type == "seqc") {
48 
+      newSce <- importSEQC(
49 
+        seqcDirs = entry$params$seqcDirs,
50 
+        samples = entry$params$samples,
51 
+        prefix = entry$params$prefix,
52 
+      )
53 
+    } else if (entry$type == "optimus") {
54 
+      newSce <- importOptimus(
55 
+        OptimusDirs = entry$params$OptimusDirs,
56 
+        samples = entry$params$samples
57 
+      )
58 
+    } else if (entry$type == "files") {
59 
+      newSce <- importFromFiles(assayFile = entry$params$assayFile,
60 
+                                annotFile = entry$params$annotFile,
61 
+                                featureFile = entry$params$featureFile,
62 
+                                assayName = entry$params$assayName)
63 
+    } else if (entry$type == "example") {
64 
+      newSce <- importExampleData(dataset = entry$params$dataset)
65 
+    } else if (entry$type == "rds") {
66 
+      importedrds <- readRDS(entry$params$rdsFile)
67 
+      if (base::inherits(importedrds, "SummarizedExperiment")) {
68 
+        newSce <- importedrds
69 
+      } else if (base::inherits(importedrds, "Seurat")) {
70 
+        newSce <- convertSeuratToSCE(importedrds)
71 
+      } else {
72 
+        stop("The '.rds' file should contain a 'SingleCellExperiment' or 'Seurat' object.")
73 
+      }
74 
+    }
75 
+    sceObjs = c(sceObjs, list(newSce))
76 
+  }
77 
+
78 
+  return(combineSCE(sceList = sceObjs,
79 
+                    by.r = NULL,
80 
+                    by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
81 
+                    combined = T)
82 
+  )
83 
+}
84 
+